metaImport error

[Darwin Chang]

I'm having issues with loading the test data onto cbioportal. Here is the full log along with the command. 

$ ~/cbioportal/core/src/main/scripts/importer/metaImport.py -s ~/cbioportal/core/src/test/scripts/test_data/study_es_0 -u http://localhost:8080 -o -v

Starting validation...

DEBUG: -: Requesting info from portal at 'http://localhost:8080'

DEBUG: -: Requesting cancer-types from portal at 'http://localhost:8080'

DEBUG: -: Requesting genes from portal at 'http://localhost:8080'

DEBUG: -: Requesting genesets from portal at 'http://localhost:8080'

DEBUG: -: Requesting genesets_version from portal at 'http://localhost:8080'

DEBUG: -: Requesting gene-panels from portal at 'http://localhost:8080'

DEBUG: meta_cancer_type.txt: Starting validation of meta file

INFO: meta_cancer_type.txt: Validation of meta file complete

DEBUG: meta_clinical_patients.txt: Starting validation of meta file

INFO: meta_clinical_patients.txt: Validation of meta file complete

DEBUG: meta_clinical_samples.txt: Starting validation of meta file

INFO: meta_clinical_samples.txt: Validation of meta file complete

DEBUG: meta_cna_discrete.txt: Starting validation of meta file

INFO: meta_cna_discrete.txt: Validation of meta file complete

DEBUG: meta_cna_hg19_seg.txt: Starting validation of meta file

INFO: meta_cna_hg19_seg.txt: Validation of meta file complete

DEBUG: -: Retrieving chromosome lengths from '/Users/darwinchang/cbioportal/core/src/main/scripts/importer/chromosome_sizes.json'

DEBUG: meta_cna_log2.txt: Starting validation of meta file

INFO: meta_cna_log2.txt: Validation of meta file complete

DEBUG: meta_expression_median.txt: Starting validation of meta file

INFO: meta_expression_median.txt: Validation of meta file complete

DEBUG: meta_expression_median_Zscores.txt: Starting validation of meta file

INFO: meta_expression_median_Zscores.txt: Validation of meta file complete

DEBUG: meta_fusions.txt: Starting validation of meta file

INFO: meta_fusions.txt: Validation of meta file complete

DEBUG: meta_gene_panel_matrix.txt: Starting validation of meta file

INFO: meta_gene_panel_matrix.txt: Validation of meta file complete

DEBUG: meta_gistic_genes_amp.txt: Starting validation of meta file

INFO: meta_gistic_genes_amp.txt: Validation of meta file complete

DEBUG: -: Retrieving chromosome lengths from '/Users/darwinchang/cbioportal/core/src/main/scripts/importer/chromosome_sizes.json'

DEBUG: meta_gsva_pvalues.txt: Starting validation of meta file

INFO: meta_gsva_pvalues.txt: Validation of meta file complete

DEBUG: meta_gsva_scores.txt: Starting validation of meta file

INFO: meta_gsva_scores.txt: Validation of meta file complete

DEBUG: meta_methylation_hm27.txt: Starting validation of meta file

INFO: meta_methylation_hm27.txt: Validation of meta file complete

DEBUG: meta_mutational_signature.txt: Starting validation of meta file

INFO: meta_mutational_signature.txt: Validation of meta file complete

DEBUG: meta_mutations_extended.txt: Starting validation of meta file

INFO: meta_mutations_extended.txt: Validation of meta file complete

DEBUG: meta_resource_definition.txt: Starting validation of meta file

INFO: meta_resource_definition.txt: Validation of meta file complete

DEBUG: meta_resource_patient.txt: Starting validation of meta file

INFO: meta_resource_patient.txt: Validation of meta file complete

DEBUG: meta_resource_sample.txt: Starting validation of meta file

INFO: meta_resource_sample.txt: Validation of meta file complete

DEBUG: meta_resource_study.txt: Starting validation of meta file

INFO: meta_resource_study.txt: Validation of meta file complete

DEBUG: meta_structural_variants.txt: Starting validation of meta file

INFO: meta_structural_variants.txt: Validation of meta file complete

DEBUG: meta_study.txt: Starting validation of meta file

INFO: meta_study.txt: Validation of meta file complete

DEBUG: -: Study Tag file found. It will be validated.

DEBUG: meta_treatment_ec50.txt: Starting validation of meta file

INFO: meta_treatment_ec50.txt: Validation of meta file complete

DEBUG: meta_treatment_ic50.txt: Starting validation of meta file

INFO: meta_treatment_ic50.txt: Validation of meta file complete

DEBUG: data_cancer_type.txt: Starting validation of file

INFO: data_cancer_type.txt: line 1: New disease type will be added to the portal; value encountered: 'brca-es0'

INFO: data_cancer_type.txt: Validation of file complete

INFO: data_cancer_type.txt: Read 1 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_clinical_samples.txt: Starting validation of file

INFO: data_clinical_samples.txt: Validation of file complete

INFO: data_clinical_samples.txt: Read 847 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_resource_definition.txt: Starting validation of file

INFO: data_resource_definition.txt: Validation of file complete

INFO: data_resource_definition.txt: Read 4 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_resource_sample.txt: Starting validation of file

INFO: data_resource_sample.txt: Validation of file complete

INFO: data_resource_sample.txt: Read 4 lines. Lines with warning: 0. Lines with error: 0

DEBUG: study_tags.yml: Starting validation of study tags file

INFO: study_tags.yml: Validation of study tags file complete.

DEBUG: -: Validating case lists

DEBUG: case_lists/cases_custom.txt: Starting validation of meta file

INFO: case_lists/cases_custom.txt: Validation of meta file complete

DEBUG: case_lists/cases_cna.txt: Starting validation of meta file

INFO: case_lists/cases_cna.txt: Validation of meta file complete

DEBUG: case_lists/cases_sequenced.txt: Starting validation of meta file

INFO: case_lists/cases_sequenced.txt: Validation of meta file complete

DEBUG: case_lists/cases_test.txt: Starting validation of meta file

INFO: case_lists/cases_test.txt: Validation of meta file complete

DEBUG: case_lists/cases_cnaseq.txt: Starting validation of meta file

INFO: case_lists/cases_cnaseq.txt: Validation of meta file complete

INFO: -: Validation of case list folder complete

DEBUG: data_gene_panel_matrix.txt: Starting validation of file

INFO: data_gene_panel_matrix.txt: line 1: This column can be replaced by a 'gene_panel' property in the respective meta file; value encountered: 'gistic'

INFO: data_gene_panel_matrix.txt: Validation of file complete

INFO: data_gene_panel_matrix.txt: Read 21 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_cna_discrete.txt: Starting validation of file

INFO: data_cna_discrete.txt: Validation of file complete

INFO: data_cna_discrete.txt: Read 9 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_cna_pd_annotations.txt: Starting validation of file

INFO: data_cna_pd_annotations.txt: lines [2, 3, 6, (1 more)]: column 4: Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint; values encountered: ['Class 2', 'Class 1']

INFO: data_cna_pd_annotations.txt: Validation of file complete

INFO: data_cna_pd_annotations.txt: Read 8 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_clinical_patients.txt: Starting validation of file

INFO: data_clinical_patients.txt: Validation of file complete

INFO: data_clinical_patients.txt: Read 845 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_expression_median.txt: Starting validation of file

INFO: data_expression_median.txt: Validation of file complete

INFO: data_expression_median.txt: Read 7 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_expression_median_Zscores.txt: Starting validation of file

INFO: data_expression_median_Zscores.txt: Validation of file complete

INFO: data_expression_median_Zscores.txt: Read 6 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_fusions.txt: Starting validation of file

INFO: data_fusions.txt: Validation of file complete

INFO: data_fusions.txt: Read 6 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_mutational_signature.txt: Starting validation of file

INFO: data_mutational_signature.txt: Validation of file complete

INFO: data_mutational_signature.txt: Read 61 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_treatment_ec50.txt: Starting validation of file

INFO: data_treatment_ec50.txt: Validation of file complete

INFO: data_treatment_ec50.txt: Read 11 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_treatment_ic50.txt: Starting validation of file

INFO: data_treatment_ic50.txt: Validation of file complete

INFO: data_treatment_ic50.txt: Read 11 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_gistic_genes_amp.txt: Starting validation of file

INFO: data_gistic_genes_amp.txt: Validation of file complete

INFO: data_gistic_genes_amp.txt: Read 13 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_gsva_pvalues.txt: Starting validation of file

INFO: data_gsva_pvalues.txt: Validation of file complete

INFO: data_gsva_pvalues.txt: Read 8 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_gsva_scores.txt: Starting validation of file

INFO: data_gsva_scores.txt: Validation of file complete

INFO: data_gsva_scores.txt: Read 8 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_cna_log2.txt: Starting validation of file

INFO: data_cna_log2.txt: Validation of file complete

INFO: data_cna_log2.txt: Read 8 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_methylation_hm27.txt: Starting validation of file

INFO: data_methylation_hm27.txt: Validation of file complete

INFO: data_methylation_hm27.txt: Read 9 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_mutations_extended.maf: Starting validation of file

INFO: data_mutations_extended.maf: lines [4, 5, 6, (5 more)]: column 164: Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint; values encountered: ['Class 2', 'Class 1', 'Class 4', '(1 more)']

INFO: data_mutations_extended.maf: lines [7, 9]: Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA]; value encountered: 'Silent'

INFO: data_mutations_extended.maf: Validation of file complete

INFO: data_mutations_extended.maf: Read 35 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_resource_patient.txt: Starting validation of file

INFO: data_resource_patient.txt: Validation of file complete

INFO: data_resource_patient.txt: Read 4 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_resource_study.txt: Starting validation of file

INFO: data_resource_study.txt: Validation of file complete

INFO: data_resource_study.txt: Read 2 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_cna_hg19.seg: Starting validation of file

INFO: data_cna_hg19.seg: Validation of file complete

INFO: data_cna_hg19.seg: Read 10 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_structural_variants.txt: Starting validation of file

INFO: data_structural_variants.txt: Validation of file complete

INFO: data_structural_variants.txt: Read 46 lines. Lines with warning: 0. Lines with error: 0

INFO: -: Validation complete

#######################################################################

Everything looks good. Importing study now

#######################################################################

Data loading step using /Users/darwinchang/cbioportal/scripts/target/scripts-3.6.6-SNAPSHOT.jar

Checked DB schema version: (expected: 2.12.8) (found: 2.12.8)

Loading cancer types...

ABORTED!

org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'coExpressionServiceImpl': Unsatisfied dependency expressed through field 'molecularDataService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'molecularDataServiceImpl': Unsatisfied dependency expressed through field 'sampleService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'sampleServiceImpl': Unsatisfied dependency expressed through field 'studyService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'studyServiceImpl': Unsatisfied dependency expressed through field 'cancerTypeService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cancerTypeServiceImpl': Invocation of init method failed; nested exception is java.util.NoSuchElementException: No value present

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:643)

at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:130)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:399)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1422)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:594)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517)

at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323)

at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226)

at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321)

at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:895)

at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:878)

at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:550)

at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:144)

at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:95)

at org.mskcc.cbio.portal.util.SpringUtil.initDataSource(SpringUtil.java:67)

at org.mskcc.cbio.portal.scripts.ImportTypesOfCancers.load(ImportTypesOfCancers.java:71)

at org.mskcc.cbio.portal.scripts.ImportTypesOfCancers.run(ImportTypesOfCancers.java:62)

at org.mskcc.cbio.portal.scripts.ConsoleRunnable.runInConsole(ConsoleRunnable.java:145)

at org.mskcc.cbio.portal.scripts.ImportTypesOfCancers.main(ImportTypesOfCancers.java:122)

Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'molecularDataServiceImpl': Unsatisfied dependency expressed through field 'sampleService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'sampleServiceImpl': Unsatisfied dependency expressed through field 'studyService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'studyServiceImpl': Unsatisfied dependency expressed through field 'cancerTypeService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cancerTypeServiceImpl': Invocation of init method failed; nested exception is java.util.NoSuchElementException: No value present

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:643)

at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:130)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:399)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1422)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:594)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517)

at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323)

at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226)

at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321)

at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)

at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1306)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1226)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:640)

... 19 more

Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'sampleServiceImpl': Unsatisfied dependency expressed through field 'studyService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'studyServiceImpl': Unsatisfied dependency expressed through field 'cancerTypeService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cancerTypeServiceImpl': Invocation of init method failed; nested exception is java.util.NoSuchElementException: No value present

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:643)

at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:130)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:399)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1422)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:594)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517)

at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323)

at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226)

at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321)

at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)

at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1306)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1226)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:640)

... 32 more

Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'studyServiceImpl': Unsatisfied dependency expressed through field 'cancerTypeService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cancerTypeServiceImpl': Invocation of init method failed; nested exception is java.util.NoSuchElementException: No value present

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:643)

at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:130)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:399)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1422)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:594)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517)

at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323)

at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226)

at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321)

at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)

at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1306)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1226)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:640)

... 45 more

Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cancerTypeServiceImpl': Invocation of init method failed; nested exception is java.util.NoSuchElementException: No value present

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:160)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:416)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1788)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:595)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517)

at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323)

at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226)

at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321)

at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)

at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1306)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1226)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:640)

... 58 more

Caused by: java.util.NoSuchElementException: No value present

at java.util.Optional.get(Optional.java:135)

at org.cbioportal.service.impl.CancerTypeServiceImpl.getParent(CancerTypeServiceImpl.java:76)

at org.cbioportal.service.impl.CancerTypeServiceImpl.initPrimarySiteMap(CancerTypeServiceImpl.java:35)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:389)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:333)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:157)

... 70 more

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Error occurred during data loading step. Please fix the problem and run this again to make sure study is completely loaded.

Traceback (most recent call last):

  File "/Users/darwinchang/cbioportal/core/src/main/scripts/importer/metaImport.py", line 217, in <module>

    cbioportalImporter.main(args)

  File "/Users/darwinchang/cbioportal/core/src/main/scripts/importer/cbioportalImporter.py", line 533, in main

    process_directory(jvm_args, study_directory, args.update_generic_assay_entity)

  File "/Users/darwinchang/cbioportal/core/src/main/scripts/importer/cbioportalImporter.py", line 337, in process_directory

    import_cancer_type(jvm_args, data_filename)

  File "/Users/darwinchang/cbioportal/core/src/main/scripts/importer/cbioportalImporter.py", line 67, in import_cancer_type

    run_java(*args)

  File "/Users/darwinchang/cbioportal/core/src/main/scripts/importer/cbioportal_common.py", line 962, in run_java

    raise RuntimeError('Aborting due to error while executing step.')

RuntimeError: Aborting due to error while executing step.

[Pim van Nierop]

Hello Darwin,

There appears to be a problem with the cancer types in the database. Can you provide us with the steps that you performed to arrive at the error. A list of commands that you executed would suffice. This would help us to reproduce and analyze your problem.

All the best,

Pim van Nierop  

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Pim van Nierop

Software Engineer / cBioPortal specialist

E p...@thehyve.nl

T +31(0)30 700 9713

M +31(0)6 29464525

W thehyve.nl

    

[Darwin Chang]

Hello Pim,

Seems like you were right. As I was going along your deploy without Docker steps, I stumbled upon this error. I believe this is how I load the database onto cbioportal, but cannot understand what the problem is.

$ cd ~/cbioportal/db-scripts/src/main/resources/

$ mysql --user=cbio_user --password=somepassword cbioportal < seed-cbioportal_hg19_v2.7.3.sql 

mysql: [Warning] Using a password on the command line interface can be insecure.

ERROR 1054 (42S22) at line 275: Unknown column 'CYTOBAND' in 'field list'

Any help would be appreciated,

Very Respectfully,

Darwin Chang

[Darwin Chang]

Sorry, missed a line between the cd and the second mysql command, 

$ mysql --user=cbio_user --password=somepassword cbioportal < cgds.sql

mysql: [Warning] Using a password on the command line interface can be insecure.

[Pim van Nierop]

Hello Darwin,

Is your problem solved now and can we mark this thread as completed?

All the best,

Pim

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/5884de13-2e0d-4a52-a9a4-b1fed64e14a2n%40googlegroups.com.

[Darwin Chang]

Hello Pim,

I still get an error when running these lines

$ cd ~/cbioportal/db-scripts/src/main/resources/

$ mysql --user=cbio_user --password=somepassword cbioportal < cgds.sql

mysql: [Warning] Using a password on the command line interface can be insecure.

$ mysql --user=cbio_user --password=somepassword cbioportal < seed-cbioportal_hg19_v2.7.3.sql 

mysql: [Warning] Using a password on the command line interface can be insecure.

ERROR 1054 (42S22) at line 275: Unknown column 'CYTOBAND' in 'field list'

Like you said, I think it has to do with the database, but I can't seem to load it onto my computer.

Darwin Chang

[Pim van Nierop]

Hello Darwin,

I understand that you chose the installation method that does not user Docker. I must stress here that we do not recommend this way of deployment since this makes it much more difficult to help you solve problems. Is there a particular reason why you chose not to user the docker-compose deployment method? 

I found out that in order to install MySQL v5.7 on my system I have to remove the preinstalled MySQL version which is rather difficult to do. I will forward your question to the cBioPortal backend team so that they can look into you rissue.

All the best,
Pim

[Benjamin Gross]

Hi Darwin, Pim,

I’m looking at the following doc: https://github.com/cBioPortal/datahub/tree/master/seedDB

and it says when using a cBioPortal release version > 2.0.0, a migration step to a new database schema might be required.

Can you try migrating the database after importing the schema but before you import the seed database?  The migration process is described here:

https://github.com/cBioPortal/cbioportal/blob/master/docs/Updating-your-cBioPortal-installation.md#running-the-migration-script

Let us know how it goes.

Benjamin

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/7b026b22-4c24-404f-aa9e-d12f879c5a75n%40googlegroups.com.

[Darwin Chang]

Hello Pim,

I am actually stuck at the same step for both with and without Docker. 

Docker error: 

$ docker run -it --rm --net cbio-net -v "$PWD/study/cSCC:/study:ro" -v "$PWD:/outdir" -v "$PWD/portal.properties:/cbioportal/portal.properties:ro" cbioportal/cbioportal:latest metaImport.py -u http://cbioportal-container:8080 -s $PWD/study/cSCC --html=/outdir/report.html -v -o

directory cannot be found: /Users/darwinchang/study/cSCC

Hello Benjamin,

I did the steps you mentioned a while ago, but did it again just in case.

$ cd ~/cbioportal/core/src/main/scripts/

$ python migrate_db.py --properties-file ~/cbioportal/src/main/resources/portal.properties --sql ~/cbioportal/db-scripts/src/main/resources/migration.sql

WARNING: This script will alter your database! Be sure to back up your data before running.
Continue running DB migration? (y/n) y
Everything up to date, nothing to migrate.
Finished.

Let me know if I am missing anything.

Darwin Chang

[Pim van Nierop]

Hello Darwin,

You docker run command is not correct. The -s flag for the metaImport.py command is from the perspective of the container and should be /study. This makes the following command:

$ docker run -it --rm --net cbio-net -v "$PWD/study/cSCC:/study:ro" -v "$PWD:/outdir" -v "$PWD/portal.properties:/cbioportal/portal.properties:ro" cbioportal/cbioportal:latest metaImport.py -u http://cbioportal-container:8080 -s /study/ --html=/outdir/report.html -v -o

Can you try that?

All the best,

Pim

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/9f4fe15b-4e49-4f0d-8afe-e67820d8def0n%40googlegroups.com.

[Darwin Chang]

Hello Pim, 

Seems like that did the trick! I got a study status of "Available". 

I was wondering if this is the process we need to use to get our dataset loaded potentially on the cbioportal.org website, or if this some type of local version. We are looking to load it onto the website, but I do not see it after performing the steps below.

Darwin CHang